How do bacteria regulate their metabolism?

A global control mechanism adapts bacteria to changing environments

2017-11-29 – News from the Physics Department

A fundamental prerequisite for life on earth is the ability of living
organisms to adapt to changing environmental conditions. Physicists at
the Technical University of Munich (TUM) and the University of
California San Diego (UCSD) have now determined that the regulation
mechanisms used by bacteria to adapt to different environments are based
on a global control process that can be described in a single
equation.

Microbiological cultures are kept in flasks that are stirred in a water
bath at constant temperature. The researchers then change the bacteria’s
nutrients and observe how they adapt. Countless experiments were
required to uncover the global control mechanism.
– Photo: Johannes Wiedersich / TUM

On earth parameters like temperature, light conditions, availability of
food and many other essential aspects of the environment fluctuate in
time and vary from place to place. Life as we know it is only possible,
because nature has the means to deal with many types of such
environmental fluctuations. Each cell and every organism relies on
countless mechanisms to adapt.

Professor Ulrich Gerland explains: “This is especially true for
bacteria, which cannot shape their environment or migrate large
distances. They have to more or less cope with their environment as it
is.”

One of the best studied model systems is Escherichia coli, a bacterium
which lives in the gut of mammals, including humans. It has to adapt to
the constantly changing nutrients that flow by, and produce specific
enzymes only when needed. For instance, the enzymes that break down the
milk sugar lactose are only needed when lactose is actually present;
other enzymes that help synthesize, e.g., certain amino acids, are only
required when these amino acids are missing.

Escherichia coli adapt to different food supplies

In the lab scientists study these adaptations of the microorganisms by
changing the nutrition of bacteria – i.e. the composition of the brew
in which they nourish. It is well established, and earned Jacques Monod
a Nobel Prize in 1965, that bacteria adapt to the current environment by
regulating the expression (and thus the number of copies) of particular
proteins. Thus, depending on environmental factors, the concentrations
of different proteins are adjusted.

A cross-section of a small part of an Escherichia coli cell, showing only large macromolecules.
In green are the proteins that constitute the cell membrane,
proteins within the cell are blue and ribosomes,
the ‘machines’ that synthesise the proteins as required, are purple.
A part of the cell’s nucleoid is shown in yellow and orange.
RNA, a copy of a small section of DNA used for transcription of proteins is shown in white.
– Illustration: David S. Goodsell / the Scripps Research Institute

However, despite the great interest and the tremendous research carried out over half a century,
the biochemical details of this complicated mechanism
from the bacterium sensing what is required to the actual regulation of the concentration of enzymes
are still far from fully understood.
This is not surprising, if one keeps in mind,
that even a rather “simple” bacterium as E. coli
has several thousand different kinds of proteins and other molecules (in different concentrations)
packed tightly within its tiny microscopic enclosure and a corresponding DNA containing thousands of genes.

“At present it is impossible to account for all the interactions and biochemical reactions
between all molecules present in a bacterium,” says Ulrich Gerland.
“All the biomolecules present and all reactions that take place within the cell are part of the bacterium’s metabolism.”
Bacterial growth by cell division essentially requires
that the full set of biomolecules within a cell is duplicated from scratch.

Growth transition kinetics

His team together with colleagues from the University of California at
San Diego has taken an approach that focuses on the principal mechanisms
of these regulation processes instead of looking at the molecular
details of the reaction pathways. The fundamental question the team of
researchers addressed experimentally is on how fast do bacteria adapt to
different changes of the environment?

They performed a large set of experiments where the growth conditions
for the bacteria were changed. For example, by adding a good nutrient
source after a period of poor supply of food or vice versa. At so-called
up-shifts of nutrients, the growth rate of the bacteria increases after
some lag due to the adaption process.

Other experiments induced a so-called diauxie, a phenomenon already
observed by Monod. If bacteria are fed on one type of food and later on
a different kind, growth slows or comes to a halt, although there is
always enough food present. This is due to the bacteria shifting their
digestion - i.e. the concentrations of certain enzymes - from one food
to another.

By detailed observations of different parameters during the development
of the bacterial cultures a quantitative characterization of the
temporal evolution of the regulation was achieved. As one would expect,
the different experiments yield quantitatively and qualitatively
different growth curves. The measured transition curves are specific to
the respective start parameters and to the shifts induced.

Model of flux-controlled regulation (FCR)

Model of flux-controlled regulation (FCR).
Food substrates S1 and S2 are imported by uptake proteins C1 and C2, generating food influx (1).
From the precursors (2a) derived from the food, proteins (2b) are synthesised by the ribosomes.
Each of the white numbered circles symbolizes a biochemical process involved in the overall adaptation of the cell.
– Illustration: Schink and Gerland / TUM

The scientists did not stop at these observations. In order to elucidate
the bacteria’s adaption strategy, they developed a model to describe the
phenomena from a physicist’s perspective. In a top-down approach, the
model just uses a qualitative knowledge of the biochemical details of
the regulation. It is based on balancing the flux of substances within
the bacterium, i.e. establishing equations on the flow of matter.

Several regulatory processes are considered, but it turns out that
applying the condition of a balanced flux of substances, these can be
simplified to just a single differential equation, describing the global
kinetics of the whole set of biochemical reactions involved in the
different adaptions.

“Our steady-state model of the regulation mechanism correctly describes
the temporal development of adaptation to changing nutrients, as well as
increases, reductions and changes in the available nutrients,
quantitatively and without adjustable parameters,” says Ulrich Gerland,
summarizing the results of the study.

“Apparently, the kinetics of growth adaptation do not depend on
microscopic details of the individual biochemical reactions, but rather
adhere to a global strategy for the redistribution of resources for
protein synthesis,” says Ulrich Gerland. “It is thus conceivable that our
theoretical model might be applicable to an array of similar kinetic
processes.”

The research was funded by the
National Institutes of Health (NIH), USA,
by the Simons Foundation, USA,
and
the German Research Foundation (DFG) via the
Excellence Cluster ‘Nanosystems Initiative Munich’, as well as the
priority program SPP1617.